Controlling 2.8 startup behaviour
Apparently there needs to be a "config" folder with the appropriate files inside the version folder of a locally extracted blender version (e.g. C:\BlenderTest\blender-2.80.0-git.c0c1b4542f39-windows64/2.80/) for it to ignore USER and SYSTEM settings.

Creating this folder and copying over the appropriate files "userpref.blend" and optionally "bookmarks.txt" and "recent-files.txt" isolates the respective blender.exe from the user and system settings. Any changes made from this executable are saved in the local userpref file.

See this answer for file paths under common operating systems.